AMBER Archive (2009)

Subject: [AMBER] radical simulation

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Fri Jul 24 2009 - 02:34:53 CDT

Dear all,

   Can MD simulation be used to radical system? We are going to check the water distribution around a radical molecule. Are the atomic charges obtained as the neutral molecule for radical?
As in the following example, should the electron pair on C4 atom be restraint during RESP calculation?

e.g.
REMARK
REMARK
ATOM 1 C1 MOL 1 -3.428 1.900 -0.002 1.00 0.00
ATOM 2 C2 MOL 1 -2.207 1.365 0.000 1.00 0.00
ATOM 3 N3 MOL 1 -2.383 0.036 0.001 1.00 0.00
ATOM 4 C4 MOL 1 -3.668 -0.267 -0.001 1.00 0.00
ATOM 5 N5 MOL 1 -4.308 0.887 -0.003 1.00 0.00
ATOM 6 C11 MOL 1 -5.789 0.971 -0.005 1.00 0.00
ATOM 7 C13 MOL 1 -6.191 2.459 0.008 1.00 0.00
ATOM 8 C15 MOL 1 -1.350 -0.988 0.004 1.00 0.00
ATOM 9 H17 MOL 1 -1.336 1.856 0.002 1.00 0.00
ATOM 10 H19 MOL 1 -3.648 2.876 -0.003 1.00 0.00
ATOM 11 H21 MOL 1 -6.151 0.531 -0.827 1.00 0.00
ATOM 12 H23 MOL 1 -6.155 0.515 0.806 1.00 0.00
ATOM 13 H25 MOL 1 -7.189 2.536 0.007 1.00 0.00
ATOM 14 H27 MOL 1 -5.822 2.912 -0.803 1.00 0.00
ATOM 15 H29 MOL 1 -5.825 2.897 0.830 1.00 0.00
ATOM 16 H31 MOL 1 -1.777 -1.892 0.004 1.00 0.00
ATOM 17 H33 MOL 1 -0.782 -0.888 0.821 1.00 0.00
ATOM 18 H35 MOL 1 -0.780 -0.889 -0.812 1.00 0.00
TER
 
Many thanks.

Jeffrey Yang

-----------
Dalian Institute of Chemical Physics,
Chinese Academy of Sciences
Dalian, China
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